PDB-5hgq: Loa loa Lysyl-tRNA synthetase in complex with Cladosporin.

ID or keywords:

Entry

Database: PDB / ID: 5hgq

Title

Loa loa Lysyl-tRNA synthetase in complex with Cladosporin.

Components

Lysine--tRNA ligase

Keywords

LIGASE/LIGASE INHIBITOR / Cladosporin / Lysine-tRNA synthetase / Loa loa / helminth parasites / LIGASE-LIGASE INHIBITOR complex

Function / homology

Function and homology information

Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology

Biological species

Loa loa (African eye worm)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.283 Å

Authors

Sharma, A. / Sharma, M. / Yogavel, M. / Sharma, A.

Funding support

India, 1items

Citation

Journal: PLoS Negl Trop Dis / Year: 2016
Title: Protein Translation Enzyme lysyl-tRNA Synthetase Presents a New Target for Drug Development against Causative Agents of Loiasis and Schistosomiasis
Authors: Sharma, A. / Sharma, M. / Yogavel, M. / Sharma, A.

History

Deposition	Jan 8, 2016	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Oct 26, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 23, 2017	Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5hgq.cif.gz	725.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5hgq.ent.gz	599.2 KB	Display	PDB format
PDBx/mmJSON format	5hgq.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5hgq_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	5hgq_full_validation.pdf.gz	1.4 MB	Display
Data in XML	5hgq_validation.xml.gz	68.7 KB	Display
Data in CIF	5hgq_validation.cif.gz	90.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hg/5hgq ftp://data.pdbj.org/pub/pdb/validation_reports/hg/5hgq	HTTPS FTP

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Related structure data

Related structure data	3bjuS S: Starting model for refinement
Similar structure data	7ea9-1 6ka6-2 5zh4-d 3bju-3 3a74-1 6wbd-d 4pg3-2 1bbu-1 6aqh-6 6kct-2 5zh5-d 3e9h-1 4pg3-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Lysine--tRNA ligase

D: Lysine--tRNA ligase

B: Lysine--tRNA ligase

C: Lysine--tRNA ligase

hetero molecules

242 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Lysine--tRNA ligase

B: Lysine--tRNA ligase

hetero molecules

defined by author&software
121 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Lysine--tRNA ligase

C: Lysine--tRNA ligase

hetero molecules

defined by author&software
121 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	120.165, 147.355, 160.944
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Lysine--tRNA ligase / Lysyl-tRNA synthetase Mass: 60077.238 Da / Num. of mol.: 4 / Fragment: UNP residues 78-599 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Loa loa (African eye worm) / Gene: LOAG_03217 / Plasmid: pETM41 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: E1FQP0, lysine-tRNA ligase
#2: Chemical	ChemComp-LYS / LYSINE Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₅N₂O₂
#3: Chemical	ChemComp-KRS / cladosporin / (3R)-3-[[(2R,6S)-6-methyloxan-2-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one Mass: 292.327 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₆H₂₀O₅
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.17 Å³/Da / Density % sol: 61.22 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, magnesium chloride, spermidine / PH range: 8

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 10, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 3.28→50 Å / Num. obs: 40374 / % possible obs: 91.9 % / Redundancy: 3.3 % / R_merge(I) obs: 0.239 / Net I/σ(I): 4.44
Reflection shell	Resolution: 3.3→3.36 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.82 / % possible all: 91.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3BJU

3bju

Resolution: 3.283→43.754 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2923	1996	4.96 %	Random selection
R_work	0.2536	-	-	-
obs	0.2556	40253	90.84 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.283→43.754 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14500	0	130	7	14637

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	14991
X-RAY DIFFRACTION	f_angle_d	0.909	20361
X-RAY DIFFRACTION	f_dihedral_angle_d	11.153	8864
X-RAY DIFFRACTION	f_chiral_restr	0.06	2250
X-RAY DIFFRACTION	f_plane_restr	0.008	2632

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.2828-3.3649	0.3652	121	0.3381	2330	X-RAY DIFFRACTION	79
3.3649-3.4558	0.3616	144	0.3154	2776	X-RAY DIFFRACTION	93
3.4558-3.5575	0.3358	143	0.2998	2735	X-RAY DIFFRACTION	93
3.5575-3.6723	0.2933	143	0.2863	2748	X-RAY DIFFRACTION	92
3.6723-3.8034	0.3297	144	0.2679	2761	X-RAY DIFFRACTION	93
3.8034-3.9556	0.2956	144	0.2726	2761	X-RAY DIFFRACTION	93
3.9556-4.1355	0.311	144	0.2582	2756	X-RAY DIFFRACTION	92
4.1355-4.3534	0.3062	144	0.228	2771	X-RAY DIFFRACTION	93
4.3534-4.6258	0.2846	145	0.2197	2771	X-RAY DIFFRACTION	92
4.6258-4.9825	0.2341	145	0.2113	2775	X-RAY DIFFRACTION	92
4.9825-5.4831	0.2655	145	0.233	2771	X-RAY DIFFRACTION	92
5.4831-6.2745	0.2997	145	0.2521	2769	X-RAY DIFFRACTION	91
6.2745-7.8977	0.2908	143	0.2591	2769	X-RAY DIFFRACTION	90
7.8977-43.7581	0.243	146	0.2307	2764	X-RAY DIFFRACTION	86

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.7301	0.2179	0.144	0.9516	-0.3064	1.1442	-0.0059	0.1832	0.0148	-0.0233	0.0845	-0.146	0.1329	0.1533	-0.0217	0.3174	0.0326	-0.0196	0.339	-0.0183	0.2368	31.518	-22.8013	-57.015
2	0.4044	-0.3765	-0.4771	0.3432	0.8046	1.1502	0.0094	0.0465	-0.1048	0.0009	0.0442	0.0044	0.0866	-0.0681	0.0017	0.3447	-0.0677	-0.0096	0.3857	0.0623	0.3974	5.001	-20.2161	-17.0509
3	0.6178	-0.2834	0.0163	0.8839	-0.1333	1.1296	0.0382	-0.0227	-0.1048	0.112	-0.0002	0.0108	0.1804	-0.1548	0.0259	0.3216	-0.0486	0.0505	0.4269	-0.0303	0.3871	-31.2788	-24.3719	-27.4941
4	0.9015	-0.3548	-0.3141	0.1745	0.0977	0.4181	0.1348	-0.0366	-0.5223	0.0417	-0.1016	0.2527	-0.1202	0.1259	-0.0069	0.3668	-0.0504	-0.0343	0.3436	-0.0453	0.2861	-19.9721	-22.4568	-41.6441
5	-0.0095	-0.0802	-0.066	1.1752	-0.5076	0.9328	-0.1425	0.0952	-0.2242	-0.1774	0.042	-0.2212	0.2338	0.1024	0.03	0.3231	-0.0013	0.0077	0.4559	0.0111	0.4489	-15.6211	-19.1548	-73.014
6	1.0583	-0.4459	-0.1097	1.0148	0.3645	0.4187	0.0785	-0.127	0.0682	0.0344	-0.0391	-0.3601	-0.0916	0.179	-0.0348	0.4384	-0.0253	0.0481	0.4355	-0.045	0.3034	4.3026	-12.1782	-58.994
7	0.5809	-0.1618	-0.3135	0.6037	0.7	0.6559	-0.1603	-0.1961	-0.0471	0.0082	0.1055	-0.0789	0.138	0.14	0.0034	0.309	0.0169	-0.037	0.374	-0.0512	0.3772	1.0341	-19.6685	-74.0036
8	0.5217	-0.3907	0.0961	0.2818	0.0003	0.301	0.0435	0.0025	-0.1583	0.0801	0.3044	0.1807	-0.092	-0.1174	-0.0202	0.4132	-0.0093	0.004	0.238	0.0217	0.3865	8.3708	4.564	4.4883
9	0.6763	-0.0538	-0.0223	1.0166	0.4125	0.6217	0.0624	0.0071	0.2839	0.1246	-0.0792	-0.226	-0.0754	-0.0566	-0.0163	0.2882	0.0363	-0.0125	0.4829	0.1065	0.3514	11.7074	10.1391	7.4313
10	0.2309	0.0994	-0.3842	0.5389	-0.4246	0.92	0.0036	-0.3156	0.091	0.1065	0.077	0.09	0.1702	0.2539	-0.0528	0.3698	-0.0182	-0.053	0.498	-0.043	0.3309	25.9714	-14.5618	-11.4984
11	0.2059	0.0692	0.2551	0.6868	0.3138	0.9424	-0.1298	-0.0847	0.1697	0.4554	0.0143	0.111	0.0597	0.1576	-0.0034	0.4455	0.0236	-0.0314	0.4966	-0.0591	0.3548	29.0088	-25.8156	-24.1085
12	0.5813	-0.3759	0.3121	0.3221	0.1404	0.6601	0.1422	-0.2091	0.1185	0.1742	-0.0889	-0.1623	-0.1042	0.1603	-0.034	0.3747	-0.0202	-0.0289	0.4922	0.0035	0.5654	49.8015	-17.3716	-21.9833
13	0.3347	0.122	0.4052	0.848	0.1671	0.7196	0.1283	0.0754	-0.2847	0.3104	-0.0213	-0.2144	0.2237	-0.3738	-0.0275	0.3009	0.0807	-0.0406	0.4454	0.002	0.5854	45.8893	-27.347	-26.8381
14	0.9011	-0.1924	-0.7238	0.6921	0.1998	0.56	0.3177	-0.4316	0.4858	0.2987	0.1452	-0.5628	0.2164	0.1552	0.0878	0.3851	0.0153	-0.0121	0.405	-0.0402	0.5085	33.1336	-20.7974	-20.9137
15	0.2814	0.4399	0.3533	0.8459	0.1217	1.2667	0.0581	0.0907	0.0519	-0.1498	0.0755	-0.1955	-0.1722	-0.1093	-0.008	0.3298	-0.0094	-0.0616	0.4274	-0.0359	0.3949	-10.4421	10.415	-90.0455
16	0.4676	0.381	-0.8825	0.5436	-0.3212	0.339	0.0004	0.235	0.0191	-0.0707	0.0255	0.1874	0.0094	-0.0688	0.0147	0.3236	0.0205	-0.067	0.4172	-0.0376	0.4041	-37.3306	-18.4671	-63.888
17	0.0834	-0.1344	-0.0528	0.2172	0.1168	0.082	0.2073	-0.0057	-0.1041	-0.0754	-0.0544	0.0793	0.0484	0.2616	0.1934	0.3541	0.1283	-0.1305	0.313	-0.1165	0.2973	0.1066	-21.4177	-42.0555

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 139 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 140 through 505 )
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 6 through 122 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 123 through 192 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 193 through 278 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 279 through 337 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 338 through 505 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 5 through 57 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 58 through 139 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 140 through 219 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 220 through 278 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 279 through 372 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 373 through 463 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 464 through 507 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 7 through 133 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 134 through 505 )
17	X-RAY DIFFRACTION	17	(chain 'A' and resid 601) or (chain 'B' and resid 601) or (chain 'C' and resid 601) or (chain 'D' and resid 602)

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